Contacts of the helix formed by residues 84 - 93 (chain c) in PDB entry 3J7Y
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER 84 (chain c).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83c PHE* 1.3 75.5 - - - +
85c LEU* 1.3 59.3 + - - +
86c ASP* 3.5 3.6 - - - -
87c LEU* 3.1 37.7 - - - +
88c LEU* 3.0 27.4 + - - +
205c SER* 4.1 12.6 - - - -
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Residues in contact with LEU 85 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69c HIS* 3.7 15.9 - - + +
72c ILE* 4.0 24.9 - - + +
73c GLN* 3.5 46.0 - - + +
76c GLY* 5.9 2.9 - - - -
83c PHE* 3.9 15.0 - - + +
84c SER* 1.3 70.3 - - - +
86c ASP* 1.3 69.8 + - - +
87c LEU 3.3 0.2 - - - -
88c LEU* 4.0 7.7 - - + +
89c LYS* 3.1 34.0 + - - +
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Residues in contact with ASP 86 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84c SER* 3.5 4.0 - - - -
85c LEU* 1.3 82.1 + - - +
87c LEU* 1.3 60.7 + - - +
89c LYS* 3.8 10.0 + - - +
90c THR* 3.6 25.5 + - - +
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Residues in contact with LEU 87 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84c SER* 3.1 27.4 + - - +
85c LEU 3.3 0.4 - - - -
86c ASP* 1.3 78.8 - - - +
88c LEU* 1.3 60.3 + - - +
90c THR* 2.7 22.6 + - - +
91c ALA* 3.7 3.6 + - - +
125c LEU* 4.1 6.9 - - + +
201c ALA* 3.4 41.8 - - + +
204c GLN* 3.5 31.9 - - + +
205c SER* 5.2 2.9 - - - +
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Residues in contact with LEU 88 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72c ILE* 3.8 31.4 - - + +
75c PHE* 4.4 8.5 - - + -
83c PHE* 3.5 33.9 - - + -
84c SER 3.0 17.4 + - - +
85c LEU* 4.0 7.4 - - + +
86c ASP 3.4 0.2 - - - -
87c LEU* 1.3 73.9 - - - +
89c LYS* 1.3 56.7 + - - +
91c ALA* 2.8 35.5 + - + +
92c PHE* 3.4 30.3 - - + -
198c VAL* 4.1 26.9 - - + +
201c ALA* 4.5 7.8 - - + +
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Residues in contact with LYS 89 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68c TYR* 4.2 17.0 + - + -
69c HIS* 3.9 44.3 + - - +
72c ILE* 3.5 26.4 - - + +
85c LEU* 3.1 24.2 + - - +
86c ASP* 3.8 9.4 - - - +
88c LEU* 1.3 76.0 - - - +
90c THR* 1.3 61.7 + - + +
92c PHE* 3.2 15.1 + - - +
93c VAL* 3.6 15.6 + - - +
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Residues in contact with THR 90 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86c ASP 3.6 13.1 + - - +
87c LEU* 2.7 27.4 + - - +
89c LYS* 1.3 76.7 - - + +
91c ALA* 1.3 54.9 + - - +
92c PHE 3.2 0.9 + - - -
93c VAL* 3.3 17.5 + - + +
119c LEU* 6.2 3.1 - - + -
120c LYS* 4.3 38.5 - - + +
121c SER* 3.9 12.2 - - - +
122c ASN* 3.0 15.2 - - - +
125c LEU* 4.0 9.2 - - - +
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Residues in contact with ALA 91 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87c LEU 4.2 3.6 - - - +
88c LEU* 2.8 16.6 + - + +
90c THR* 1.3 76.5 + - - +
92c PHE* 1.3 57.9 + - - +
122c ASN* 3.0 21.7 + - - +
125c LEU* 3.9 13.2 - - + +
194c THR* 3.9 9.7 - - - +
197c ALA* 3.4 44.5 - - + +
198c VAL* 3.9 8.5 - - + +
201c ALA* 4.3 4.0 - - + -
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Residues in contact with PHE 92 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68c TYR* 3.6 4.9 - - - +
72c ILE* 3.8 28.3 - - + -
75c PHE* 4.4 9.2 - + - -
88c LEU* 3.4 48.0 - - + -
89c LYS 3.2 4.6 + - - +
90c THR 3.2 0.8 - - - -
91c ALA* 1.3 80.2 - - - +
93c VAL* 1.3 62.7 + - - +
94c ASN* 3.4 7.3 + - - -
122c ASN* 3.8 4.6 + - - +
175c VAL* 4.0 17.9 - - + -
178c LEU* 3.3 35.2 - - + -
179c THR* 3.4 31.0 - - + +
180c LEU* 3.5 32.5 + - + +
194c THR* 4.3 4.4 - - - +
198c VAL* 4.4 10.5 - - + -
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Residues in contact with VAL 93 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68c TYR* 5.4 0.9 - - - +
89c LYS* 3.6 15.7 - - + +
90c THR* 3.3 12.4 + - + +
92c PHE* 1.3 74.3 - - - +
94c ASN* 1.3 61.4 + - - +
97c TYR* 4.1 7.0 - - + -
98c ILE* 3.6 32.8 - - + -
119c LEU* 4.1 29.4 - - + -
120c LYS 5.9 0.2 - - - +
121c SER* 3.5 15.0 - - - +
122c ASN* 2.7 22.7 - - - +
180c LEU* 4.1 19.7 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il